First, the more you can keep the run dry (keep water from going in, accelerate drying-out) the less smelly it will be. See my "fixing a muddy run" page, link in .sig below, for suggestions -- usually you need to do as many of them as possible, not just 'pick one'.

Second, if it is real pooey it may not take much moisture to make it stink, so however much you can clean it will help (and if you can expand the run or reduce the chicken population in there). Also try tilling some lime into the top few inches of the soil -- plain garden lime, not quicklime. That will encourage the stinkiest of the chemical compounds to break down into less-stinky things. This is in addition to the aforementioned other steps, not instead of.

Exact same problem cropped up on us last week/s... we had days and days of rain and it just never totally dried... went and got a big ol' bag of DE from the feed store, sprinkled liberally, and all better. May give it a try.